Nonsyndromic cleft lip with or without cleft palate (nsCL/P) has a complex etiology, which involves both genetic and environmental factors. In this study, we carried out mutation screening of the poliovirus receptor related-2 (PRR2) gene, located at an orofacial cleft (OFC) linkage region 19q13 (OFC3). PRR2 Sau96I (A/G) genotypes of 212 patients with nsCLP and 221 controls were detected using a polymerase chain reaction-restriction fragment length polymerase assay. The results showed significant differences in the genotype and allele distribution of the PRR2 Sau96I (A/G) between the cases and controls. The GG genotype resulted in a significantly raised odds ratio (OR) compared with the AA genotype (OR=3.031; 95% confidence interval: 1.601, 5.742). The G allele showed a significant elevated risk (χ(2) = 26.991, p=0.000, OR=2.147; 95% confidence interval: 1.605, 2.871) compared with the A allele. Hence, our results support the hypothesis that this polymorphism contributes to the risk of nsCL/P, suggesting a possible etiologic role of PRR2 in nsCL/P.